Right, which is why I am wondering if there is another statistic that can calculate the asymmetry of divergences across a tree or something. In theory, you could have an evolutionary tree where the locations of speciation and net diversification are scattered across a tree, or you could have a phylogeny where speciation is restricted to a few, very closely related taxa whereas net diversification across the rest of the tree is negative. The implications of the two patterns are very different. We get a lot of patterns like the latter in paleontology where a group seems to be doing well in terms of raw alpha diversity, but it's generally one group exploring the morphospace of a specialized niche that is diversifying whereas the rest of the group suffers (e.g., horses in the Miocene). That is usually a sign that something is about to go wrong in the next ~10 Ma.
A colleague had suggested a statistic similar to an EDGE score might work, but the problem is that calculates evolutionary distinctiveness of a single lineage, not how asymmetrically distributed total group diversity is. The other issue is that when looking at a clade through time EDGE score is going to increase regardless as basal taxa die out and surviving clades become more and more divergent. In tetrapods, for example, all of the major living clades diverged prior to the Jurassic, which means they have huge ghost lineages to their nearest relative outside that clade and that would increase EDGE score. On Tue, Jul 23, 2024, 1:16 PM O'Meara, Brian C <bome...@utk.edu> wrote: > Hi, Russell. > > > > Across taxa/clades, sure: * clads* (Maliet et al., 2019, > https://doi.org/10.1038/s41559-019-0908-0) or *MiSSE* (Vasconcelos et > al., 2022, https://doi.org/10.1111/evo.14517) can do this. They paint > different diversification rates on different parts of the tree without > requiring a priori assignment. > > > > However, I’d be careful about interpreting rates through time, even with > these models. Louca & Pennell (2020, > https://www.nature.com/articles/s41586-020-2176-1) show that multiple > different rates can be equally likely. You could use clads or MiSSE to > paint ancestral nodes into diversification regimes, but I’d worry about how > much they actually mean. > > > > Best, > Brian > > > > _________________________________________ > > > > Brian O’Meara > > He/Him > > Professor, Dept. of Ecology & Evolutionary Biology > > University of Tennessee, Knoxville > > > > > > *From: *R-sig-phylo <r-sig-phylo-boun...@r-project.org> on behalf of > Russell Engelman <neovenatori...@gmail.com> > *Date: *Tuesday, July 23, 2024 at 8:42 AM > *To: *mailman, r-sig-phylo <r-sig-phylo@r-project.org> > *Subject: *[R-sig-phylo] Calculating Asymmetry in Speciation Across a > Phylogeny > > Dear R-Sig-Phylo, > > I was wondering if there was a way to quantitatively examine > diversification and speciation rates that is sensitive to the fact that not > all clades diversify equally? > > I have a phylogeny where the overall diversity of the group — particularly > in terms of higher level clades — declines at a specific point in time, but > the broader pattern is being covered up by a massive burst of speciation at > one ecologically stereotyped (and possibly taxonomically oversplit) node on > the tree. Raw speciation and extinction rates end up giving a biased view > of the pattern because they treat all lineages as equal and can't parse > that 6-10 clades are declining while the remaining one is undergoing > diversification. This contrasts with older parts of the tree where > diversification is more evenly spread across different clades. > > I had considered calculating a Shannon Diversity Index or Inverse Simpson's > Diversity Index at each point on a LTT after dividing the tree up by family > to get an idea of the overall balance of alpha diversity across clades over > time (i.e., clade X represents a disproportionate contribution to standing > alpha diversity as time goes on). However, this relies on dividing the tree > into a priori groups based on relatively arbitrary criteria and felt rather > hacky. I was wondering if there was a more impartial way of calculating or > quantitatively describing the asymmetry in diversification rates across > nodes over time? > > Sincerely, > Russell > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
